Monday, June 27, 2011

Leading Research Organizations Announce Top-Tier, Open Access Journal for Biomedical and Life Sciences

The Howard Hughes Medical Institute, the Max Planck Society and the Wellcome Trust announced today that they are to support a new, top-tier, open access journal for biomedical and life sciences research.

The three organizations aim to establish a new journal that will attract and define the very best research publications from across these fields. All research published in the journal will make highly significant contributions that will extend the boundaries of scientific knowledge.

A team of highly regarded, experienced and actively practicing scientists will ensure fair, swift and transparent editorial decisions followed by rapid online publication. The first issue of the journal, whose name has yet to be decided, is expected to be published in the summer of 2012.

The three research organizations developed their plans following a workshop in 2010 at HHMI's Janelia Farm Research Campus attended by a number of leading scientists. The participants concluded that there was a need for a model of academic publishing that better suits the needs of the research community.

Dr. Robert Tjian, President of the Howard Hughes Medical Institute, says: "The message from the research community was clear: we are fortunate to have many excellent journals, but there is need for a different, more appropriate and efficient publishing model."

Professor Herbert Jäckle, Vice President of the Max Planck Society, says: "A journal which aims to represent and publish the very best research outcomes needs an editorial team of experienced – and, crucially, actively practicing – scientists. It must also be editorially independent of those who provide the financial support."

Sir Mark Walport, Director of the Wellcome Trust, says: "We will attract the most outstanding science for publication by establishing a journal in which researchers have confidence in robust editorial decisions taken by their scientific peers. This will be a journal for scientists edited by scientists. The ethos of the journal will be to avoid asking authors to make extensive modifications or perform endless additional experiments before a paper can be published."

Recruitment is under way for an Editor-in-Chief who – together with the journal's editorial team – will be an experienced, active scientist. The editorial team will be editorially independent of the funders. They will rely on their scientific expertise and active research experience to identify the best papers, make scientifically-based judgments and exercise leadership in steering these papers through peer review.

The journal will employ an open and transparent peer review process in which papers will be accepted or rejected as rapidly as possible, generally with only one round of revisions, and with limited need for modifications or additional experiments. For transparency, reviewers' comments will be published anonymously.

As the journal will only exist online, it offers an opportunity to create a journal and article format that will exploit the potential of new technologies to allow for improved data presentation. The journal will be an open access journal, i.e. the entire content will be freely available for all to read, to reproduce and for unrestricted use. This open access system will also enhance opportunities to share content and to more directly engage the reader.

The three organizations have made a commitment to cover costs of launching the journal to ensure its success. The long-term business model will be developed by the incoming Editor-in-Chief and the team they build.

This is great news. The more #openaccess journals we have the better. Clearly some of the text here is a dig at existing journals, including PLoS Biology. PLoS Biology definitely needs to work on some things - like transparency (e.g., if your article is rejected, the Academic Editor who advised the professional editors is not names). PLoS Biology is also run by professional editors. Thus it is not run by "active scientists" which is another one of the comments in this press release. Personally I think it would be better if PLoS Biology was run by active scientists. But that is not the system there. I have a strange role at PLoS Biology - "Academic Editor in Chief" for a journal not run by academics. In essence I am a senior advisor to the professionals who run the journal. I personally would prefer it if academics ran the journal, probably for the same reasons that HHMI, Wellcome, and Max Planck make such a big deal out of it here. But the professionals do run PLoS Biology. And overall, they do a good job. I think the journal could certainly be better - and thus this new competition should be good. We will have to wait and see just how much competition it is. It seems a bit weird for them to call this a "top tier" journal before it exists. Maybe they should have said "aiming to be a top tier journal" or something like that. But I think it probably will become one if HHMI and Wellcome and MaxPlanck scientists start publishing their good papers there. I hope this helps catalyze some beneficial changes at PLoS Biology, but we will have to wait and see.

It is a good time for #OpenAccess when major organizations start to compete to create the best "top tier" open access journal. In the end, this can only be good for science and scientists.

And opening up the paper revealed some interesting material before one even gets to the meat of the paper:

Funding: This study was funded by the participants, by 23andMe, and by a grant from Sergey Brin. Company CEO and co-author AW, wife of SB, has provided financial support to 23andMe for its general operational needs. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: CBD, JYT, ED, AKK, EMD, UF, JLM, AW, and NE are or have been employed by 23andMe and own stock options in the company. 23andMe CEO AW has provided general guidance, including guidance related to the company's research undertakings and direction. PLoS co-founder Michael B. Eisen is a member of the 23andMe Scientific Advisory Board.

Some fascinating stuff there - and I did know some of it even though my brother, as mentioned above, is a member of the 23 and me Scientific Advisory Board. Interesting that they mention funds from Sergey Brin, stock options, and multiple roles of Anne Wojcicki. Kudos to PLoS for pushing for more disclosures - something we desperately need in science. And Kudos to 23 and me for disclosing the details here and publishing in PLoS Genetics.

Oh, and the paper seems pretty interesting too. But since I do have a bit of a conflict of interest there (with my brother and all) I am not sure I am going to write about the paper itself just yet.

Wednesday, June 22, 2011

On June 19, 2011, we had a software bug that caused authentication issues. You can read more about it in our blog post. Our records show that your account wasn't improperly logged into during this time.

We are writing to you because one or more users you share a Dropbox folder with logged into their account during that period. We have no reason to believe that the login was improper, but in the unlikely event it was, there could have been access to the information in the following shared folder:

(Name withheld by me)

We are very sorry as this never should have happened. We are implementing additional safeguards to prevent this from happening again. If you have any questions please contact us at support@dropbox.com

Tuesday, June 21, 2011

Here are some quick notes from my trip to Austin Texas for the Indoor Air 2011 meeting.

About the meeting:
I got involved in helping organize a session at this conference as part of my microBEnet project. More on the planning and the meeting later but here are some quick notes just to get them out there. I wrote a bit about the run up to the meeting in the following posts:

The meeting.
Below are some notes about the trip with twitter posts, pictures, and a few comments. I will post later with some more "scientific lessons learned" and such. But wanted to get this out there before I forgot details.

Headed out June 6.
Was going to head out June 7 but decided to head out late on June 6 so I could get to the meeting a bit earlier. I am posting my tweets below as a guide to the trip. Tweets are highlighted in yellow.

Had a two plus hour layover in Las Vegas airport. What a horrible place with all the noise, the slot machines, and such. So I finally found a place that was reasonably quiet for dinner. Plus it had the hockey game on so I was happy.

Monday, June 20, 2011

This is truly the golden era for plant sciences. One key sign of this is the announcement of the winners of the competition to become HHMI Investigators in Plant Sciences.

HHMI, the Howard Hughes Medical Institute, has for many years picked HHMI Investigators in Biomedical Research. Those picked get guaranteed funds for 5 years and become technically employees of HHMI in order to get them out of miscellaneous burdensome university activities. It's a win win situation for universities because HHMI pays for space and salaries for the Investigators. I myself tried to get me one of these "Uncle Howie" types of positions a few years ago but did not win out. My brother, Michael, did. The other people they picked the year they picked Michael and not me were all very good, so I actually did not feel so bad about not getting it.

The GBMF, aka the Gordon and Betty Moore Foundation has itself made major contributions to science and medicine in various ways. One example is the Marine Microbiology Initiative (MMI) (which funded the iSEEM project for which I am PI) and cool work out of many top marine labs. In fact, the MMI program did something rarely seen outside of HHMI - they funded "people not projects" by creating MMI Investigators who got a good chunk of money to do pretty much whatever they wanted.

Thus it was great to hear some time ago that GBMF and HHMI were coming together to create a Plant Sciences Investigator program. I confess even though I am not a real plant biologist I considered applying for this because I have shifted much of my work recently into studies of plant associated microbiomes. But I did not apply. And I kept wondering - who would emerge from the competition as winners. Would they be people I respected/had heard of?

Saturday, June 18, 2011

Well, just got back from Synthetic Biology 5.0 at Stanford. I don't really have time to do a thorough job with a blog post but I will try to fill in some details here.

1. Got invited by Natalie Kuldell in April to participate in an education workshop for the meeting. Eventually said yes, but only after deciding to not go to the Earth Microbiome Meeting in Beijing. I said yes in part b/c it was close by home but also b/c of the people Natalie invited to be on the panel. She wrote in the invitation email:

Other panelists who have confirmed their participation in this session are from Understanding Science/Understanding Evolution (Juday Scotchmoor), Nature Education (Ilona Miko), Science for Citizens (Darlene Cavalier), GenSpace (Ellen Jorgenson), and Hong Kong University of Science and Technology (King Chow).

And well, of the ones I knew on the list, they all were great.

2. Had a conference call (very brief) in June to discuss the session.

3. Headed out to Stanford very late Tuesday night - and thus missed the Slam session that night. I got to my hotel at about 1:30 AM.

4. I woke up early enough to hop on my bike and ride on over to the meeting. I was a PhD student at Stanford and had brought my bike in the hopes of going for some rides around town. I took some pics on the way in:

Well, if you can, for a minute, ignore that fact that in Discover Interview: Lynn Margulis Says She's Not Controversial, She's Right | Evolution | DISCOVER Magazine Discover Magazine in essence is promoting some of the refuted ideas Lynne Margulis has about HIV. Sure they hint in part that they think she is over the top but they also give her a soapbox to spout some of her latest absurdities on HIV and such. I would suggest you don't even read the main part of the Discover article. Just read Tara Smith's discussion of it: Margulis does it again : Aetiology. Margulis should not be given such prominence in a magazine like Discover. But that is not what I am hear to write about. I am hear to point out that Discover also sets up a red herring for Margulis. In the beginning of the article, it is written:

"A conversation with Lynn Margulis is an effective way to change the way you think about life. Not just your life. All life. Scientists today recognize five groups of life: bacteria, protoctists (amoebas, seaweed), fungi (yeast, mold, mushrooms), plants, and animals. Margulis, a self-described “evolutionist,” makes a convincing case that there are really just two groups, bacteria and everything else."

Seriously? Scientists today do not recognize five groups. Scientists today have moved past that to recognize and/or argue about bacteria, archaea and eukaryotes - the three domains of life. These three groups were first proposed in 1977 by Carl Woese and colleagues. Did Discover somehow miss the last 34 years of science? WTF? For setting up such an evolutionary red herring in this painful interview with Lynne Margulis, I am giving Discover Mag my coveted "Twisted tree of life award". Past winners are:

I posted this to twitter yesterday but am now adding it to my blog since it was so great. At the Synthetic Biology 5.0 meeting at Stanford I walked into the poster session last night to discover this incredible poster:

Karmella Haynes, had hand painted her poster on canvas. Drawn in by the art, I went to talk to her (well, first I said "This is awesome" or something like that. And then I found out a bit more detail. She had her paints with her and was continuing to add touches to the painting. Though I was fascinated by the art side of this, then we got to talking about the science because actually - the figures there were about work she had done on applying some ideas from synthetic biology to animal cells in tissue culture.

I was completely blown away by this. I am not sure if the same posters will be up tomorrow and if so I will try to get some better shots. Anyway, I found out she is on her way to a faculty position in Arizona and has recently been a post doctoral fellow at Davidson College.

And then with a little help from Google I discovered her openwetware page: Karmella Haynes. And from that I found her art page: http://www.karmellahaynes.com/. I hope she does more hand painted posters for conferences - it certainly brightened up the poster session and made my day.

Monday, June 13, 2011

Jason Stajich speaks Wednesday, June 29th at noon PST on "Fungal phylogenomics: Getting lost in the moldy forest."
Fungi occupy diverse ecological niches in roles from nutrient cycling in rainforest floors to aggressive plant and animal pathogens. Molecular phylogenetics has helped resolve many of branches on the Fungal tree of life and enabling studies of evolution across this diverse kingdom. The genome sequences from hundreds of fungi now permit the study of change in genes and gene content in this phylogenetic context and to connect molecular evolution with adaptation to ecological niches or changes in lifestyles. I will describe our work in studies contrasting pathogenic and non-pathogenic fungi and efforts to unravel the evolution of multicellularity in fungi comparing unicellular basal fungi with multicellular mushrooms and molds.
The development of tools for data mining and use of fungal genomics is also driving the pace of molecular biology and genetics of fungi. I will highlight new approaches to make this easier and the ways data integration can inform and transform studies of functional biology of fungi.

Japan

04:00 (04:00 AM) on Thursday, June 30

New Zealand

07:00 (07:00 AM) on Thursday, June 30

West Coast USA

12:00 (12:00 PM) on Wednesday, June 29

East Coast USA

15:00 (03:00 PM) on Wednesday, June 29

England

20:00 (08:00 PM) on Wednesday, June 29

France

21:00 (09:00 PM) on Wednesday, June 29

Learn how to connect ahead of time. To hear about upcoming talks, send an email to phyloseminar+subscribe@googlegroups.com or follow @ematsen.
If you can't make it, don't fret-- you can always watch the recording

I note - my post originally said "Wash you hands" and my 6 year old daughter was snooping at my computer and said "Daddy, it says 'wash you hands' not 'wash your hands.'" Well, I think I found a new blog editor.

I spend most of my time working on biology. I like to think I cover lots of breadth within biology and I probably do - microbes, evolution, ecology, human health, pathogens, symbioses, forensics, genomics, bioinformatics, and more. But nothing like really looking at other fields to realize how narrowly focused one is.

And that is what has happened to me since I took on the "microBEnet" project trying to foster communications and collaborations on microbiology of the built environment. I now pay much more attention to anything that might have a connection to "Building Science" in one way or another. Not only did I just go to an Indoor Air meeting, but I keep discovering more and more stuff right near home that I was not aware of before. For example - I just got sent this news link from Aaron Darling in my lab: UC Davis News & Information :: History of sciences in architecture subject of Mellon Foundation winner's study. Previously, I would definitely not have been paying much attention to architecture and history of science. But now seeing other people at UC Davis working on the Built Environment just makes me think about how I can build connections with them and talk to them about buildings (and other built environments) and possibly, one day, about the microbes that are in them.

Which brings me to another story. At the Indoor Air meeting earlier in the week in Austin, Texas, when heading to the conference center I got into a conversation with someone looking for the registration desk. After showing her where to go she asked where I was from and I said "UC Davis." And it turns out - she was too. Turns out, this was Deborah Bennett, who I had heard mentioned the evening before but had not heard the whole name. I just knew someone else at the meeting was from Davis. Deborah is at the UC Davis School of Public Health and works on some really interesting stuff. And since UC Davis is so big (some 2500 or so faculty I think) - it is not always easy or simple to find people even if you might have a connection to them.

So anyway, just a little commentary on how I find it fascinating to see for the first what was in a way right before my eyes.

Thursday, June 09, 2011

Well, I do not even have any idea what to say. I got pointed to this paper: PLoS Genetics: Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis by KamounLab on twitter. The authors of the paper include colleagues at the DOE-Joint Genome Institute so it is possible that they are baiting me to get some attention. But YHGTBFKM - the dispensome? Defined by them as "The dispensable chromosomes collectively comprise the dispensome and showed extreme plasticity during sexual reproduction." Now, I have seen my share of bad omics words (and which I write about often with, for example, my Worst New Omics Word Award and Bad Omics Word of the Day). But this is the first case where the word, and the excessive use of it in the paper is distracting (as suggested by KamounLab) to the science. Is this word really necessary? Could they not just say "dispensable chromosomes" (which I note, I might still have problems with since they would only be known as dispensable under certain conditions)? But "dispensome" is unnecessary, distracting, and, well, not a good word. Thus in this case I have decided to not even give them an award per se but to simply say that I think this is possibly the worst omics word I have ever seen. I note - I am not criticizing the science (nor endorsing it mind you) they did here. But the word, oh the word. It hurts me. It really does.

Wednesday, June 08, 2011

So a few Saturday's ago I was at the Davis Farmer's Market and Steve Smit from Mt. Moriah Farm's showed me this pic that a photographer had given him. Steve is one of my favorite people anywhere. I don't know why really. But I go to the Farmer's Market many times just to see him/buy stuff from him. He is funny, warm, interesting, social, etc. And apparently a photographer caught one of our interactions from earlier this year.

Fortunately, she put her name on the back of the picture and a little googling and I found her photo collection on flickr. Her name is Rhonda Roman and I really like her collections there. But in particular I love this picture she took of me and Steven and others at the Market. It captures everything really about my interactions with Steve. Thanks Rhonda. A picture is worth way way more than 1000 words.

Not much detail there I know - but in essence the plan is to build a partnership between UC Davis and BGI with BGI provided genomics and informatics expertise and capabilities and Davis providing biological expertise and diversity (of course, Davis has some genomics chops too and BGI does some biology but you probably get the point).

For those who do not know, BGI is a relative newcomer on the block in terms of large scale genomics research institutes. But by being new they have had a massive advantage in a way in that they are really the first to be developed as a "Second-generation Genome Center" having been built / developed with the new second generation sequencing systems at its core. Thus while other large centers around the world have tried to adapt to the new second generation sequencing systems, BGI started from scratch and could build it's enterprise around the new systems.

I am excited about the possible connections with BGI though I confess I do not know a whole lot about the plans. There have been lots of whisperings here at Davis about building a partnership with BGI and people have been a bit nervous about word getting out too early. So, though I have heard some details I have not been an active part of the discussions. However, whatever the plans are I am looking forward to interactions with BGI. They are really pushing the frontiers of genome sequencing in many ways. And despite the moans and groans from many people, I do not think genome sequencing is on a downward slope in any way. For example, as a tool in studying microbes, genome sequencing still has many many years of use - after all there are hundreds of millions of microbial species that have yet to be studied and each one has lots of intraspecific diversity (e.g., across geography) to be characterized.

This development is just one of many that make me impressed with the new UC Davis Administration. Ever since Chancellor Katehi came on board I have been pleased with almost every major initiative and development and administrative hire on campus. Sure - the budget cuts from the California government hurt. But in challenging times, you need great leadership. And we certainly have it at UC Davis these days. And if you think I am just sucking up, you should read some of the things I wrote about our previous administration. I really am impressed here.

I do not know what will happen with the BGI - UC Davis partnership. Right now it is just a plan. But I will do what I can to help it succeed and I am looking forward to interactions with BGI and the bright future at UC Davis.

Monday, June 06, 2011

Well, off to Austin for a meeting I would not have imagined going to a few years ago. Indoor Air 2011. Why am I going? Because a few years ago I began to discuss studying the microbiology of the built environment with Paula Olsiewski, from the Alfred P. Sloan Foundation. You see, the Sloan Foundation has a new program in this area "The Indoor Environment". Eventually, after much discussion I applied for a grant in their program. My grant is a bit unusual (for me and for others probably) in that it focuses on communication, coordination, networking, collaboration, etc.

My project is called "microBEnet" - which stands for "microbiology of the Built Environment network". The BE is purposefully capitalized to emphasize the Built Environment part and we figure, since microbes are small, the m should be lower case. For more on the project see: Microbiology of the Built Environment Network | Site for the microBEnet project. As part of this project, a collaborator (Hal Levin) and I are doing many activities and I will post more about them over time. Among our activities are a new blog, and a diversity of resources.

Which brings me to Indoor Air 2011. We are also starting to organize or help organize some meetings and workshops to bring together the various folks who might be interested in microbiology of the built environment. And for Indoor Air we have helped the meeting organizer Rich Corsi plan some sessions on microbiology of the built environment. The sessions take place Wednesday and Thursday and should be great. Looking forward to going to Austin, maybe seeing some friends at UT and nearby (hint hint Dr. Hillis, Sheril K, etc) and learning about the built environment.

Edited by Frans J. de Bruijn these two volumes are the most comprehensive coverage of metagenomics out there right now. The chapters are almost overwhelming (full disclosure, I have two chapters in here - both of which are republications of Open Access papers I have published on metagenomics). See below for full chapter lists.

But now it seems as though there has been a resurrection of sorts (I guess I should have paid attention in March). See for example: SRA Home where it is stated that

"Recently, NCBI announced that due to budget constraints, it would be discontinuing its Sequence Read Archive (SRA) and Trace Archive repositories for high-throughput sequence data. However, NIH has since committed interim funding for SRA in its current form until October 1, 2011. In addition, NCBI has been working with staff from other NIH Institutes and NIH grantees to develop an approach to continue archiving a widely used subset of next generation sequencing data after October 1, 2011.

We now plan to continue handling sequencing data associated with:

RNA-Seq, ChIP-Seq, and epigenomic data that are submitted to GEO

Genomic and Transcriptomic assemblies that are submitted to GenBank

Genomic assemblies to GenBank/WGS

16S ribosomal RNA data associated with metagenomics that are submitted to GenBank

In addition, NCBI will continue to provide access to existing SRA and Trace Archive data for the foreseeable future. NCBI is also continuing to discuss with NIH Institutes approaches for handling other next-generation sequencing data associated with specific large-scale studies."

I was at a committee meeting yesterday for a great PhD student here at UC Davis, Michael Hornsby and the topic of selfish DNA came up. After his meeting we sat down and looked for some new papers and review papers on the topic. I just thought it might be of value to share some of these here:

I am working on a few proposals to the National Science Foundation where NSF asks one to include "lists of institutions, project personnel, and collaborators with Conflicts of Interest".

Seems simple I suppose. But not when you get down to the details. For example I found some guidance from the NSF about this where they ask one to list coauthors, collaborators, co-editors, students, advisors, advisees, friends, relatives, and many other affiliations.

To make a very long story short. NSF wants you to make a list of anyone who possibly should not review your grant. And if you are involved in many large collaborative projects or teach or train a lot of students. Well, you are screwed. For example, if they really want me to be thorough, I would probably have to list more than 500 people. This would include a few hundred co-authors and hundreds of collaborators (e.g., on some projects I am working on with the Joint Genome Institute there are hundreds of people involved in some way).

Wednesday, June 01, 2011

Well, sad as it may be I finally made it into the basement in the building where I have worked for five + years - the Genome and Biomedical Sciences Facility (GBSF) at UC Davis (the Genome Center is in the same building). There, down in the basement they were having an Open House for the CMGI - the Center for Molecular and Genomic Imaging. I knew of some of the stuff they did but had never been down to see their facility and their, well, toys. And it was really cool.

They also had a nice food spread upstairs on the first floor of our building that I discovered later. The best part of this spread were the animal chocolates and carvings:

Well, thanks to @yokofakun (Pierre Lindenbaum) and #gepasi (Pedro Mendes) on twitter I found out about the announcement from the Public Library of Science (PLoS) yesterday that they have opened up a search application programming interface (API) to allow outside users better access to PLoS searching (see the PLoS blog: PLoS API). This is a great step for PLoS and should accelerate the ways that people access and search for content at PLoS. For more information see: